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This example shows sample raw dataa report table, trial design and results data for the in vitro Neutral Red Uptake Cytotoxicity Assay in example study 123. 

Expand
titleStudy 123, Report Table

The following shows the tabulated data as it is represented in a report table for this study 123.  This report includes summary statistics (e.g. Average, Standard Deviation, Coeff. Var.) for each plate and an EC50 value for the entire assay. The grey cells in plate 1 are cells that do not contain the CHO Hamster cells. 

Neutral Red Cytotoxicity Assay Results (Relative Absorbance Data)

Run-Port Number




Sample ID

Smoke

Fraction

Regime

Replicate Number

Plate Number

Well Number


Relative Assay Plate Absorbance Readings




Cigarette Smoke Condensate (µg/mL)

SLS (µg/mL)


EC50 (µg/ml)

0

10

50

75

100

120

140

160

200

110

200

0
1-1



030001

A
Medium

1

1

1

0.046*

0.046*0.039*0.012*0.030*0.003*0.057*0.032*0.003*0.050*0.044*

0.040*

1-1



030001

A
Medium

1

1

2

0.048*

107

77.7

65.7

30.2

15.6

9.79

5.41

2.49

8.09

0.791

0.014*

1-1



030001

A
Medium

1

1

3

0.005*

98.6

77.4

57.7

35.8

8.09

7.36

3.22

0.791

6.38

0.061

0.050*

1-1



030001

A
Medium

1

1

4

0.049*

94.9

81.5

38.2

31.2

7.60

5.17

3.22

0.791

5.17

0.304

0.017*

1-1



030001

A
Medium

1

1

5

0.047*

111

78.1

64.5

32.9

8.82

5.90

2.74

1.28

10.3

0.547

0.011*

1-1



030001

A
Medium

1

1

6

0.032*

96.6

76.2

48.0

26.8

7.84

4.20

2.74

1.52

8.09

4.93

0.022*

1-1



030001

A
Medium

1

1

7

0.044*

105

77.9

58.2

28.3

8.09

4.68

1.76

0.547

8.57

1.76

0.056*

1-1



030001

A
Medium

1

1

8

0.056*

0.013*0.040*0.008*0.013*0.002*0.029*0.018*0.006*0.016*0.024*

0.046*


Average


101

78.2

54.5

29.9

9.70

6.17

3.37

1.19

8.94

1.22



Std. Dev.


6

2.9

9.4

3.6

2.95

2.19

1.12

0.72

2.72

1.58



Coeff. Var.


5.8

3.6

17.2

11.9

30.4

35.5

33.1

61.0

30.5

129.9



*media without cells

1-1















030001

A
Medium

1

2

1


93.4

74.0

56.0

35.1

11.8

8.70

5.10

1.98

5.34

1.02

1-1




030001

A
Medium

1

2

2


102

75.2

53.3

35.1

11.8

7.74

5.58

3.66

5.34

1.02

1-1




030001

A
Medium

1

2

3


107

79.0

55.0

26.5

10.1

6.06

3.66

1.74

7.02

0.780

1-1




030001

A
Medium

1

2

4


104

80.2

55.3

29.8

8.94

3.90

3.66

1.50

6.30

0.780

1-1




030001

A
Medium

1

2

5


101

75.7

54.1

26.7

4.86

4.38

1.26

1.02

6.30

1.02

1-1




030001

A
Medium

1

2

6


110

85.7

67.7

26.0

5.34

4.62

3.42

1.50

6.30

0.540




030001

1-1

030001

A

Medium

1

2

7


104

77.8

64.9

27.7

8.22

3.18

2.46

1.02

6.30

0.780

1-1




030001

A
Medium

1

2

8


103

71.6

58.9

25.5

9.42

4.14

3.90

1.26

4.38

0.780



Average


103

77.4

58.1

29.0

8.82

5.34

3.63

1.71

5.91

0.840



Std. Dev.


5

4.4

5.3

4.0

2.63

1.97

1.37

0.86

0.83

0.170



Coeff. Var.


4.6

5.6

9.2

13.6

29.8

36.9

37.6

50.0

14.1

20.2



EC50 (µg/ml). Effective concentration at 50% cytotoxicity.  (using a specific sigmoidal equation = model). (could also be EC20 or EC30, EC70, etc.)













123

Dataset wrap
Rowcaps
Rows 1-2:Show two records for TSPARMCD = "GLPTYP", using TSSEQ to indicate multiple records, since both GLP Types apply for this example study. 
Row 8:Shows that the sponsor's study reference ID is not applicable.
Rows 9-12:Show that TSGRPID has been used to link records (name, location, country) related to the test facility (TSGRPID = 1). The Study Director is associated with the Test Facility.
Rows 18-24:Show that this example study includes two different species of bacteria and a total of five strains. 
Rows 18-22:Show that TSGRPID (TSGRPID = 2) has been used to link the information for one species (Salmonella) with four different strains that are tested in this example study.
Rows 23-24:Show that TSGRPID (TSGRPID = 3) has been used to link the information for one species (Escherichia coli) with the strain that is tested in this example study.
Expand
titlets.xpt (trial summary, study level parameters)
  • Assumption: The intent of this dataset is to provide a summary of trial (study) information. This is not subject-level data. 
  • Assumption: A Trial (study) can have more than one assay type
  • Assumption: ASSAYID value of ALL indicates that it applies to all assays in the study

Row

STUDYID

ASSAYID

DOMAIN

TSSEQ

TSGRPID

TSPARMCD

TSPARM

TSVAL

TSVALNF

Dataset2
  • Assumption: A Trial (study) can have more than one assay type
Expand
titlets.xpt (trial summary, study level parameters)

Row

STUDYID

ASSAYID

DOMAIN

TSSEQ

TSGRPID

TSPARMCD

TSPARM

TSVAL

TSVALNF

1123NRUTS1
GLPTYPGood Laboratory Practice TypeFDA
2123NRUTS2
GLPTYPGood Laboratory Practice TypeOECD
3123NRUTS1
STSTDTCStudy Start Date2022-05-25
4123NRUTS1
STITLEStudy Title

Determination of the in vitro genotoxicity potential using the in vitro Neutral Red Uptake assay


5123NRUTS1
SNDIGVERSEND Implementation Guide VersionTOBACCO IMPLEMENTATION GUIDE VERSION 1.0
6123NRUTS1
SNDCTVERSEND Controlled Terminology VersionSEND Terminology 2021-09-30
7123NRUTS1
SSPONSORSponsor OrganizationExample
Applicant
Sponsor Inc.
8123NRUTS1
SPREFIDSponsor Study Reference ID
NOT APPLICABLE
9123NRUTS11TSTFNAMTest Facility NameExample
Tox Testing
Test Lab Name
10123NRUTS11TSTFLOCTest Facility Location10 Somewhere Street, Montgomery, AL 10000
11123NRUTS11TFCNTRYTest Facility CountryUSA
12123NRUTS11STDIRStudy DirectorDr. R. Smith
13123NRUTS1
GLPFLGLP FlagY
14123NRUTS1
ASTDAssay StandardNIH Publication No. 07-4519
15123NRUTS1
ASTDVAssay Standard Version2006-11
16123NRUTS1
SSTYPStudy TypeGENOTOXICITY IN VITRO
17123NRUTS1
SSSTYPStudy Sub TypeIn Vitro Neutral Red Uptake
18123NRUTS1
SPECIESSpeciesHamster
19123NRUTS1
TESTSYSTest SystemCHO
ITVTYPE
(CT e.g, Product, positive control, negative control, vehicle control, solvent control)
Expanddataset-wrap
titletx.xpt (trial sets)
Rowcaps
Rows 1-20:Show the test conditions for the set with a short name or SETCD value of CSC-50b.  The sponsor chose this value to represent plate number 1, well number 1, with a concentration of 50µg/mLof Cigarette Smoke Condensate as shown in the report table for study 123.
Row 17:Shows the value for STRAIN/SUBSTRAIN is NO STRAIN because the well is a media only well, having no CHO Hamster cells. 
Rows 21-40:Show the test conditions for the set with a short name or SETCD value of CSC-50.  The sponsor chose this value to represent plate number 1, well number 2, with a concentration of 50µg/mLof Cigarette Smoke Condensate as shown in the report table for study 123.
Rows 41-60:Show the test conditions for the set with a short name or SETCD value of CSC-50.  The sponsor chose this value to represent both wells numbered 7 in plate number 1 and 2, with a concentration of 110µg/mLof Sodium Laurel Sulfate as shown in the report table for study 123
Dataset2
  • Assumption: The Trial Sets (TX) domain provides the list of distinct sets of subjects having different experimental factors, treatment factors, inherent characteristics, or distinct sponsor applicant designations as specified in the trial design.
  • During CT definition/reviews will decide appropriate TXPARM and TXVAL; Treatment duration may be controlled;  For now, we just include good example values based on our experience
  • Where are the details of the smoke regime defined/submitted today? (e.g., puff profile = Bell shaped puffing volumes; Puff Block = 50%, etc.)
  • Smoke fraction?  is this indicator of processing of material from smoke machine..we used Smoke Exposure System - ok?
  • Incubate cells (37 ºC ±1 ºC, 90% ±10% humidity, and 5% ±1% CO2/air) - these are ranges, do we model for ranges?
Rows 1-20: Show the values for the 
Row
STUDYID
ASSAYID
DOMAIN
SETCD
SET
(what sponsor calls it)
TXSEQ
TXPARMCD
TXPARM
TXVAL
1123NRUTXCSC-50bCSC-50-blank1TRTDMINTreatment Duration Minimum47.5
2123NRUTXCSC-50bCSC-50-blank

2

TRTDTRGTreatment Duration Target48
3123NRUTXCSC-50bCSC-50-blank3TRTDMAXTreatment Duration Maximum48.5
4123NRUTXCSC-50bCSC-50-blank4TRTDUTreatment Duration UnitHOURS
5123NRUTXCSC-50bCSC-50-blank5INCBTMPIncubation Temperature37
6123NRUTXCSC-50bCSC-50-blank6INCBTMPUIncubation Temperature UnitC
7123NRUTXCSC-50bCSC-50-blank7WAVELGTHSpectrophotometer  WAVELENGTH IN NANOMETERS540
8123NRUTXCSC-50bCSC-50-blank8HUMIDAtmospheric Relative Humidity  Percent90
9123NRUTXCSC-50bCSC-50-blank9ATMCO2Atmospheric CO2 Percent5
10123NRUTXCSC-50bCSC-50-blank10SPTOBID

Sponsor defined tobacco identifier

CIG01a
11123NRUTXCSC-50bCSC-50-blank11EXPTYP

Exposure Type

Air Liquid Interface
12123NRUTXCSC-50bCSC-50-blank12SAMTYPSample TypeWhole Smoke Conditioned Media
13123NRUTXCSC-50bCSC-50-blank13INTRVNName of the Intervention ArticleTobacco ProdA
14123NRUTXCSC-50bCSC-50-
blank		14
blank14ITVTYPEtype of intervention articlePRODUCT
15123NRUTXCSC-50bCSC-50-blank15ITVCONCintervention concentration50
16123NRUTXCSC-50bCSC-50-blank16ITVCONCUintervention unitug/ml
17123NRUTXCSC-50bCSC-50-blank17STRAINStrain/SubstrainNO STRAIN
18123NRUTXCSC-50bCSC-50-blank18SPDEVIDSponsor defined device identifierPUFFMASTER3k
19123NRUTXCSC-50bCSC-50-blank19DUREFIDSmoking RegimeMedium Intensity Regimen
20123NRUTXCSC-50bCSC-50-blank20SPTOBID

Sponsor defined tobacco identifier

CIG01a
1
21123NRUTXCSC-50CSC-501TRTDMINTreatment Duration Minimum47.5
2
22123NRUTXCSC-50CSC-502TRTDTRGTreatment Duration Target48
3
23123NRUTXCSC-50CSC-503TRTDMAXTreatment Duration Maximum48.5
4
24123NRUTXCSC-50CSC-504TRTDUTreatment Duration UnitHOURS
5
25123NRUTXCSC-50CSC-505INCBTMPIncubation Temperature37
6
26123NRUTXCSC-50CSC-506INCBTMPUIncubation Temperature UnitC
7
27123NRUTXCSC-50CSC-507WAVELGTHSpectrophotometer  WAVELENGTH IN NANOMETERS540
8
28123NRUTXCSC-50CSC-508HUMIDAtmospheric Relative Humidity  Percent90
9
29123NRUTXCSC-50CSC-509ATMCO2Atmospheric CO2 Percent5
10
30123NRUTXCSC-50CSC-5010SPTOBID

Sponsor defined tobacco identifier

CIG01a
11
31123NRUTXCSC-50CSC-5011EXPTYP

Exposure Type

Air Liquid Interface
12
32123NRUTXCSC-50CSC-5012SAMTYPSample TypeWhole Smoke Conditioned Media
13
33123NRUTXCSC-50CSC-5013INTRVNName of the Intervention ArticleTobacco ProdA
14
34123NRUTXCSC-50CSC-5014ITVTYPE
(CT e.g, Product, positive control, negative control, vehicle control, solvent control)
type of intervention articlePRODUCT 
15
35123NRUTXCSC-50CSC-5015ITVCONCintervention concentration50
16
36123NRUTXCSC-50CSC-5016ITVCONCUintervention unitug/ml
17
37123NRUTXCSC-50CSC-5017STRAINStrain/SubstrainCHO
18
38123NRUTXCSC-50CSC-5018SPDEVIDSponsor defined device identifierPUFFMASTER3k
19
39123NRUTXCSC-50CSC-5019DUREFIDSmoking RegimeMedium Intensity Regimen
20
40123NRUTXCSC-50CSC-5020SPTOBID

Sponsor defined tobacco identifier

CIG01a
21
41123NRUTXSLS-110SLS-1101TRTDMINTreatment Duration Minimum47.5
22
42123NRUTXSLS-110SLS-1102TRTDTRGTreatment Duration Target48
23
43123NRUTXSLS-110SLS-1103TRTDMAXTreatment Duration Maximum48.5
24
44123NRUTXSLS-110SLS-1104TRTDUTreatment Duration UnitHOURS
25
45123NRUTXSLS-110SLS-1105INCBTMPIncubation Temperature37
26
46123NRUTXSLS-110SLS-1106INCBTMPUIncubation Temperature UnitC
27
47123NRUTXSLS-110SLS-1107WAVELGTHSpectrophotometer  WAVELENGTH IN NANOMETERS540
28
48123NRUTXSLS-110SLS-1108HUMIDAtmospheric Relative Humidity  Percent90
29
49123NRUTXSLS-110SLS-1109ATMCO2Atmospheric CO2 Percent5
30
50123NRUTXSLS-110SLS-11010SPTOBID

Sponsor defined tobacco identifier

CIG01a
31
51123NRUTXSLS-110SLS-11011EXPTYP

Exposure Type

Air Liquid Interface
32
52123NRUTXSLS-110SLS-11012SAMTYPSample TypeLiquid
33
53123NRUTXSLS-110SLS-11013INTRVNName of the Intervention ArticleSodium Laurel Sulfate
34
54123NRUTXSLS-110SLS-11014ITVTYPE
(CT e.g, Product, positive control, negative control, vehicle control, solvent control)
type of intervention articlePOSITIVE CONTROL
35
55123NRUTXSLS-110SLS-11015ITVCONCintervention concentration200
36
56123NRUTXSLS-110SLS-11016ITVCONCUintervention unitug/ml
37
57123NRUTXSLS-110SLS-11017STRAINStrain/SubstrainCHO
38
58123NRUTXSLS-110SLS-11018SPDEVIDSponsor defined device identifierPUFFMASTER3k
39
59123NRUTXSLS-110SLS-11019DUREFIDSmoking RegimeMedium Intensity Regimen
40
60123NRUTXSLS-110SLS-11020SPTOBID

Sponsor defined tobacco identifier

CIG01a



Expand
titlerelref.xpt


Image AddedImage Removed

relref.xpt

Row

STUDYID

ASSAYID

SETCD

REFTYPE

REFID

PARENT

LEVEL

1123NRUALLASSAY123NRU
1
2123NRU

CSC-50b

TRIAL SET1-3b123NRU2
3123NRU

CSC-50b

EXPERIMENTAL UNIT1-3-A1-3b3
5123NRU

CSC-50b

EXPERIMENTAL UNIT1-3-H1-3b3
6123NRUCSC-50TRIAL SET1-3123NRU2
7123NRUCSC-50EXPERIMENTAL UNIT1-3-B1-33
8123NRUCSC-50EXPERIMENTAL UNIT1-3-C1-33
9123NRUSLS-110TRIAL SET1-10123NRU2
10123NRUSLS-110TRIAL SET2-10123NRU2
11123NRUSLS-110EXPERIMENTAL UNIT1-10-G1-103
12123NRUSLS-110EXPERIMENTAL UNIT2-10-G2-103
Expand
titlegt.xpt (similar to LB)

cells growing in plate, treat cells in the plate, then add NRU dye, then extract NRU (the OBUID) dye and transfer to another plate (put in spectrophotometer & read).

  • row 161: This shows the EC50 result value for the entire assay (the SETCD, EUID, and OBUID are null).


Rows 1, 4:  These data are not shown in the above data report table but included here for completeness of the NRU assay.

RowSTUDYIDASSAYIDDOMAINGTSEQREFIDGTTESTCDGTTESTGTORRESGTORRESUGTCOLSRT (coll. summ. result type)GTSTRESCGTSTRESNGTSTRESU
1123NRUGT11-3-BABSORBAbsorbance Reading1.7 (0.0 - 2.0)

1.71.7
2123NRUGT21-3-BBKCABSBackground Corrected Absorbance Reading

1.6




1.61.6
3123NRUGT31-3-BRELABSRelative Absorbance Reading77.7%
77.777.7%
4123NRUGT41-3-CABSORBAbsorbance Reading1.8 (0.0 - 2.0)

1.81.8
5123NRUGT51-3-CBKCABSBackground Corrected Absorbance Reading

1.7




1.71.7

123NRUGT61-3-CRELABSRelative Absorbance Reading77.4

77.477.4

123NRUGT71-3RELABSRelative Absorbance Reading 78.2%MEAN78.278.2%




81-3RELABSRelative Absorbance Reading 2.9%STANDARD DEVIATION2.92.9%




91-3RELABSRelative Absorbance Reading 3.6
COEFFICIENT OF VARIANCE3.63.6




101-10-GABSORBAbsorbance Reading0.7

0.70.7




111-10-GBKCABSBackground Corrected Absorbance Reading

0.6




0.6


0.6



80123NRUGT111-10-GRELABSRelative Absorbance Reading8.57

8.578.57




121-10RELABSRelative Absorbance Reading

8.94

%MEAN

8.94

8.94






131-10RELABSRelative Absorbance Reading

2.72

%

STANDARD DEVIATION

2.72

2.72


...


141-10RELABSRelative Absorbance Reading

30.5


COEFFICIENT OF VARIANCE

30.5

30.5






152-10-GABSORBAbsorbance Reading0.9








162-10-GBKCABSBackground Corrected Absorbance Reading

0.8







160123NRUGT172-10-GRELABSRelative Absorbance Reading6.30

6.306.30

123NRUGT182-10RELABSRelative Absorbance Reading

5.91

%MEAN

5.91

5.91



123NRUGT192-10RELABSRelative Absorbance Reading

0.83

%

STANDARD DEVIATION

0.83

0.83



123NRUGT202-10RELABSRelative Absorbance Reading

14.1


COEFFICIENT OF VARIANCE

14.1

14.1


161123NRUGT21123NRUEC50Effective Concentration of 50 Percent Cytotoxicity123ug/ml
123123ug/ml